Do you have some sort of interal framework? I think you mentioned that but I can't really see what it is in your picture. I have some ideas but an interal frame might rule some of them out.
I would not use an epoxy to coat the interior walls of your cage if you want to show off the natural veneer of the baltic birch plywood. Most clear epoxies are really not a cabinet quality finish.
The bartop epoxies are not bad. If you've ever eating at an Outback Steakhouse (or many other national chains for that matter) you've seen the bartop epoxies on their tables. They have a bit of a plastic look but don't look too bad on wood. The clear solvent based epoxies can yellow a bit and also get a slightly distorted look when they shrink or flex, something you'll likely see with a 3/8" carcass.
Now, regarding glass. I assume the track your are using clamps onto the glass panels somehow? In that case tempered will work fine. I think laminated safety glass is a better choice but if the track you have isolates the edges of your glass then tempered should be okay.
Personally I think that if you make the floor and the first few inches of the cage walls more durable you'll be "good enough". The catalyed lacquer should be okay for the walls and is easy to reapply down the road if you have problems.
How you deal with the floor really depends on the design of your cage.
For the type of tracks where the glass edge slides right on a plastic or metal surface I definately think laminated safety glass is the way to go.
I'll take another look at the link your provided for your track and see if I can tell.
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Current snakes:
0.0.1 Gonyosoma oxycephala - Java locale (green)
1.2 Gonyosoma oxycephala - Jave local (green)
2.2 Gonyosoma janseni - Seleyar locale (all black)
1.2 Gonyosoma janseni - Celebes locale (Black & Tan)